What species are in the swath data?
|
SP_CODE
|
SPECIES
|
|
AGCL
|
Agarum clathratum
|
|
ALES
|
Alaria esculenta
|
|
ANSP
|
Anomia
|
|
APPA
|
Aplidium pallidum
|
|
ASDI
|
Ascophyllum nodosum
|
|
BLD
|
UNID Juv Laminariales
|
|
BOHA
|
Bonnemaisonia hamifera
|
|
BOSC
|
Botryllus schlosseri
|
|
BOVI
|
Botrylloides violaceus
|
|
BUSP
|
Bugulina spicata
|
|
BUTU
|
Crisularia turrita
|
|
CF
|
Crepidula fornicata
|
|
CHCR
|
Chondrus crispus
|
|
CIIN
|
Ciona intestinalis
|
|
CISA
|
Ciona savignyi
|
|
CLCI
|
Clathromorphum circumscriptum
|
|
CLSP
|
Cliona
|
|
CO
|
Corallina officinalis
|
|
COF
|
Codium fragile
|
|
COPE
|
Colpomenia peregrina
|
|
COTR
|
Coccotylus truncatus
|
|
CREB
|
Crisia eburnea
|
|
CRSP
|
Ceramium
|
|
CYPU
|
Cystoclonium purpureum
|
|
DEAC
|
Desmarestia aculeata
|
|
DECA
|
Dendrodoa carnea
|
|
DEMU
|
Dendrobeania murrayana
|
|
DEVI
|
Desmarestia viridis
|
|
DIAL
|
Didemnum albidum
|
|
DIAT
|
Diatom Tube Mat
|
|
DIP
|
Diplosoma listerianum
|
|
DIVE
|
Didemnum vexillum
|
|
DUCO
|
Dumontia contorta
|
|
EC
|
Encrusting coralline
|
|
EUCR
|
Euthora cristata
|
|
FG
|
Filamentous Green
|
|
HADU
|
Halisarca dujardinii
|
|
HAPA
|
Halichondria (Halichondria) panicea
|
|
HATO
|
Halosiphon tomentosus
|
|
HIRU
|
Hildenbrandia rubra
|
|
HJ
|
Dasysiphonia japonica
|
|
HYSP
|
Hymedesmia
|
|
ISAL
|
Stenosemus albus
|
|
ISRU
|
Boreochiton ruber
|
|
LADI
|
Laminaria digitata
|
|
LESP
|
Leptophytum acervatum
|
|
LEUC
|
Leucosolenia
|
|
LIGL
|
Lithothamnion
|
|
LISP
|
Lithophyllum
|
|
LIVE
|
Patinella verrucaria
|
|
MAST
|
Mastocarpus stellatus
|
|
MEMA
|
Membranipora membranacea
|
|
MOMO
|
Modiolus modiolus
|
|
MYED
|
Mytilus edulis
|
|
OBSP
|
Obelia
|
|
OSED
|
Ostrea edulis
|
|
PAPA
|
Palmaria palmata
|
|
PHRU
|
Phycodrys rubens
|
|
PHSP
|
Phymatolithon
|
|
POLS
|
Polysiphonia
|
|
PORO
|
Polyides rotunda
|
|
PORS
|
Porphyra
|
|
PTSE
|
Ptilota serrata
|
|
RAT
|
Red Algal Turf
|
|
SADE
|
Saccorhiza dermatodea
|
|
SCUN
|
Schizoporella unicornis
|
|
SE
|
Thylacodes
|
|
SL
|
Saccharina latissima
|
|
SLJ
|
Saccharina latissima
|
|
SPRE
|
Spermothamnion repens
|
|
TETE
|
Testudinalia testudinalis
|
|
TISP
|
Titanoderma
|
|
TRIN
|
Tricellaria inopinata
|
|
TUV
|
Tubular Ulvoid
|
|
UEC
|
Unidentified Erect Coralline
|
|
UFR
|
Unidentified Filamentous Red
|
|
URB
|
Unidentified Red Blade
|
|
UV
|
Blady Ulvoid
|
Let’s Plot Trends
Here are some functions we’ll apply to each species. I’ll then fit mixed models with all of them using
COUNT ~ YEAR * SITE + (1|TRANSECT)
with a gaussian error. Note, it’s count, so, I could use Poisson, but, that needs to be way more tuned to each model - this should be fine for a first cut?
Here’s how we’ll do it:
tseries_plot <- function(adf){
ggplot(adf,
aes(y = PERCENT_COVER, x = YEAR,
color = TRANSECT)) +
geom_point() +
geom_line() +
facet_wrap(~SITE, nrow = 2) +
labs(color = "Transect",
y = "Percent Cover", x = "Year",
title = adf$SPECIES[1])
}
tseries_fun <- function(adf){
betareg(I(PERCENT_COVER/100+0.001) ~ YEAR * SITE,
data = adf)
}
generate_output <- function(adf){
cat(paste0("## ", adf$SP_CODE[1], " ", adf$SPECIES[1], " \n<br>"))
tseries_plot(adf) %>% print()
if(sum(adf$PERCENT_COVER>3) > 5){
tseries_fun(adf) %>%
car::Anova(test.statistic = "Chisq") %>%
tidy() %>%
knitr::kable("html", digits = 3) %>%
kableExtra::kable_styling() %>%
print
}
cat("\n\n")
}
Now let’s purrr::walk() through the whole shebang.
walk(split(upc, upc$SP_CODE), generate_output)
AGCL Agarum clathratum
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
0.462
|
0.497
|
|
SITE
|
2
|
5.507
|
0.064
|
|
YEAR:SITE
|
2
|
1.066
|
0.587
|
ALES Alaria esculenta

ANSP Anomia
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
0.871
|
0.351
|
|
SITE
|
2
|
3.207
|
0.201
|
|
YEAR:SITE
|
2
|
2.328
|
0.312
|
APPA Aplidium pallidum

ASDI Ascophyllum nodosum

BLD UNID Juv Laminariales

BOHA Bonnemaisonia hamifera

BOSC Botryllus schlosseri

BOVI Botrylloides violaceus
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
5.444
|
0.020
|
|
SITE
|
2
|
2.257
|
0.324
|
|
YEAR:SITE
|
2
|
0.077
|
0.962
|
BUSP Bugulina spicata
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
6.022
|
0.014
|
|
SITE
|
2
|
0.462
|
0.794
|
|
YEAR:SITE
|
2
|
0.921
|
0.631
|
BUTU Crisularia turrita
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
3.092
|
0.079
|
|
SITE
|
2
|
0.343
|
0.842
|
|
YEAR:SITE
|
2
|
0.097
|
0.953
|
CF Crepidula fornicata
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
9.444
|
0.002
|
|
SITE
|
2
|
63.926
|
0.000
|
|
YEAR:SITE
|
2
|
0.214
|
0.899
|
CHCR Chondrus crispus
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
10.223
|
0.001
|
|
SITE
|
2
|
119.432
|
0.000
|
|
YEAR:SITE
|
2
|
3.597
|
0.166
|
CIIN Ciona intestinalis

CISA Ciona savignyi

CLCI Clathromorphum circumscriptum
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
2.547
|
0.110
|
|
SITE
|
2
|
1.801
|
0.406
|
|
YEAR:SITE
|
2
|
1.134
|
0.567
|
CLSP Cliona

CO Corallina officinalis
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
3.424
|
0.064
|
|
SITE
|
2
|
106.352
|
0.000
|
|
YEAR:SITE
|
2
|
1.522
|
0.467
|
COF Codium fragile

COPE Colpomenia peregrina

COTR Coccotylus truncatus

CREB Crisia eburnea

CRSP Ceramium

CYPU Cystoclonium purpureum
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
1.789
|
0.181
|
|
SITE
|
2
|
2.410
|
0.300
|
|
YEAR:SITE
|
2
|
2.289
|
0.318
|
DEAC Desmarestia aculeata
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
10.232
|
0.001
|
|
SITE
|
2
|
3.924
|
0.141
|
|
YEAR:SITE
|
2
|
2.590
|
0.274
|
DECA Dendrodoa carnea

DEMU Dendrobeania murrayana

DEVI Desmarestia viridis
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
13.132
|
0.000
|
|
SITE
|
2
|
0.496
|
0.780
|
|
YEAR:SITE
|
2
|
5.128
|
0.077
|
DIAL Didemnum albidum

DIAT Diatom Tube Mat

DIP Diplosoma listerianum

DIVE Didemnum vexillum
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
0.056
|
0.814
|
|
SITE
|
2
|
0.381
|
0.827
|
|
YEAR:SITE
|
2
|
4.127
|
0.127
|
DUCO Dumontia contorta

EC Encrusting coralline
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
32.596
|
0.000
|
|
SITE
|
2
|
1.045
|
0.593
|
|
YEAR:SITE
|
2
|
2.073
|
0.355
|
EUCR Euthora cristata

FG Filamentous Green

HADU Halisarca dujardinii

HAPA Halichondria (Halichondria) panicea

HATO Halosiphon tomentosus

HIRU Hildenbrandia rubra
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
13.427
|
0.000
|
|
SITE
|
2
|
2.989
|
0.224
|
|
YEAR:SITE
|
2
|
7.122
|
0.028
|
HJ Dasysiphonia japonica
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
27.225
|
0.000
|
|
SITE
|
2
|
73.019
|
0.000
|
|
YEAR:SITE
|
2
|
8.035
|
0.018
|
HYSP Hymedesmia

ISAL Stenosemus albus

ISRU Boreochiton ruber

LADI Laminaria digitata

LESP Leptophytum acervatum

LEUC Leucosolenia

LIGL Lithothamnion
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
0.195
|
0.659
|
|
SITE
|
2
|
16.656
|
0.000
|
|
YEAR:SITE
|
2
|
0.931
|
0.628
|
LISP Lithophyllum

LIVE Patinella verrucaria

MAST Mastocarpus stellatus
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
4.237
|
0.040
|
|
SITE
|
2
|
10.328
|
0.006
|
|
YEAR:SITE
|
2
|
3.973
|
0.137
|
MEMA Membranipora membranacea
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
4.647
|
0.031
|
|
SITE
|
2
|
10.508
|
0.005
|
|
YEAR:SITE
|
2
|
0.088
|
0.957
|
MOMO Modiolus modiolus

MYED Mytilus edulis

OBSP Obelia

OSED Ostrea edulis

PAPA Palmaria palmata

PHRU Phycodrys rubens

PHSP Phymatolithon
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
8.327
|
0.004
|
|
SITE
|
2
|
3.968
|
0.138
|
|
YEAR:SITE
|
2
|
0.503
|
0.778
|
POLS Polysiphonia
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
1.338
|
0.247
|
|
SITE
|
2
|
74.623
|
0.000
|
|
YEAR:SITE
|
2
|
3.383
|
0.184
|
PORO Polyides rotunda

PORS Porphyra
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
10.514
|
0.001
|
|
SITE
|
2
|
12.869
|
0.002
|
|
YEAR:SITE
|
2
|
10.198
|
0.006
|
PTSE Ptilota serrata

RAT Red Algal Turf

SADE Saccorhiza dermatodea

SCUN Schizoporella unicornis

SE Thylacodes

SL Saccharina latissima
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
0.818
|
0.366
|
|
SITE
|
2
|
20.972
|
0.000
|
|
YEAR:SITE
|
2
|
0.215
|
0.898
|
SLJ Saccharina latissima
|
term
|
df
|
statistic
|
p.value
|
|
YEAR
|
1
|
7.659
|
0.006
|
|
SITE
|
2
|
0.071
|
0.965
|
|
YEAR:SITE
|
2
|
0.041
|
0.980
|
SPRE Spermothamnion repens

TETE Testudinalia testudinalis

TISP Titanoderma

TRIN Tricellaria inopinata

TUV Tubular Ulvoid

UEC Unidentified Erect Coralline

UFR Unidentified Filamentous Red

URB Unidentified Red Blade

UV Blady Ulvoid
